except:
pass
-import sys, optparse
-print "%prog: version 2.2"
+import sys
+import optparse
+from commoncode import getConfigParser, getConfigOption, getConfigBoolOption, getConfigFloatOption
+
+print "profilebins: version 2.3"
def main(argv=None):
usage = "usage: python %prog label infile1 [--upstream infile2] [--downstream infile3] [--uplength kb] [--downlength kb] [--gene geneName] [--genes genefile] [--append] outfile"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--upstream", dest="upfilename")
- parser.add_option("--downstream", dest="downfilename")
- parser.add_option("--uplength", type="float", dest="uplength")
- parser.add_option("--downlength", type="int", dest="")
- parser.add_option("--gene", dest="gene")
- parser.add_option("--genes", dest="genefile")
- parser.add_option("--append", action="store_true", dest="doAppend")
- parser.set_defaults(upfilename=None, downfilename=None, uplength=0.0, downlength=0.0,
- gene=None, genefile=None, doAppend=False)
-
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
options.doAppend)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--upstream", dest="upfilename")
+ parser.add_option("--downstream", dest="downfilename")
+ parser.add_option("--uplength", type="float", dest="uplength")
+ parser.add_option("--downlength", type="int", dest="")
+ parser.add_option("--gene", dest="gene")
+ parser.add_option("--genes", dest="genefile")
+ parser.add_option("--append", action="store_true", dest="doAppend")
+
+ configParser = getConfigParser()
+ section = "profilebins"
+ upfilename = getConfigOption(configParser, section, "upfilename", None)
+ downfilename = getConfigOption(configParser, section, "downfilename", None)
+ uplength = getConfigFloatOption(configParser, section, "uplength", 0.0)
+ downlength = getConfigFloatOption(configParser, section, "downlength", 0.0)
+ gene = getConfigOption(configParser, section, "gene", None)
+ genefile = getConfigOption(configParser, section, "genefile", None)
+ doAppend = getConfigBoolOption(configParser, section, "doAppend", False)
+
+ parser.set_defaults(upfilename=upfilename, downfilename=downfilename, uplength=uplength, downlength=downlength,
+ gene=gene, genefile=genefile, doAppend=doAppend)
+
+ return parser
+
+
def profilebins(label, infilename, outfilename, upfilename=None, downfilename=None,
uplength=0.0, downlength=0.0, gene=None, genefile=None, doAppend=False):